Man pages for AllenInstitute/scrattch.hicat
Hierarchical Iterative Clustering Analysis for Transcriptomic data
| adjust_color | Correct duplicated colors |
| angle | Title |
| avgangle | Title |
| batch_process | Batch process |
| build_dend | Build dend |
| build_dend_harmonize | Build dend harmonize |
| build_dend_with_means | Title |
| build_tsne | Title |
| calc_tau | Calculate Tau scores for each gene |
| CanonCor | Canon cor |
| CCA | CCA |
| check_donor | Find donor clusters |
| check_neun | Check whether clusters are Neun+ or Neun- |
| check_outlier | Check for outlier clusters |
| check_qc | Check qc of numeric metric |
| clean_outliers | Title |
| collect_co_matrix | Collect co-clustering matrix from results files |
| comb_de_result | Title |
| combine_cl | combine cl |
| compare_annotate | Compare two sets of cluster assignments for the same set of... |
| compare_plot | Compare and plot two sets of cluster assignments |
| compute_knn | compute knn |
| compute_vg_stats | Compute gene expression variance statistics |
| convert_pair_matrix | Convert paired cluster comparison values to a matrix |
| convert_pair_matrix_str | Convert paired cluster comparison values to a matrix |
| cpm | Convert a matrix of raw counts to a matrix of Counts per... |
| create_pairs | Title |
| cutree_dend | Cut tree dendrogram |
| de_all_pairs | Perform all pairwise differential expression comparison... |
| DE_genes_cat_by_cl | Title |
| DE_genes_pairs | reverse-compatibility wrapper around de_selected_pairs() |
| de_genes_pairs_multiple | Title |
| DE_genes_pw | reverse-compatibility wrapper around de_all_pairs() |
| dend_lca | Dend lca |
| dend_list | Dendrogram list |
| dend_match | Dendrogram match |
| de_pair | reverse-compatibility wrapper around score_pair_stats() |
| de_pair_chisq | Perform pairwise differential detection tests using... |
| de_pair_limma | Perform pairwise DE tests using limma for a single pair of... |
| de_param | Set differential expression (DE) parameters for genes and... |
| de_score | reverse-compatibility wrapper around de_all_pairs_stats() |
| de_score_pairs | reverse-compatibility wrapper around... |
| de_selected_pairs | Perform pairwise differential gene expression tests between... |
| de_stats_all_pairs | Compute differential expression summary statistics for all... |
| de_stats_pair | Compute differential expression summary statistics based on a... |
| de_stats_selected_pairs | Compute differential expression summary statistics for... |
| display_cl | Display cluster plot |
| display_cl4 | Title |
| display_cl_markers_co.ratio | Title |
| display_cl_one_vs_others | Title |
| doubletFinder | Doublet detection in single-cell RNA sequencing data |
| edgeMaker | function to draw (curved) line between two points |
| fast_tsne | Title |
| find_doublet | Find doublet |
| find_low_quality_cl | Use DEGenes to identify clusters with few differentially... |
| find_vg | Identify high variability genes using Brennecke's method |
| findVG | reverse-compatibility wrapper around find_vg() |
| gene_dispersion | Compute dispersion for each gene in a gene x sample matrix |
| gene_gene_cor_conservation | Title |
| gene_loess_fit | Compute dispersion-mean Loess-fit for each gene in a gene x... |
| gene_loess_fit_z | Compute dispersion z scores for the residuals of a loess fit |
| gene_means | Compute means for each gene in a gene x sample matrix |
| gene_vars | Compute variance for each gene in a gene x sample matrix |
| gene_z | Compute dispersion z-scores for each gene in a gene x sample... |
| get_beta_score | Title |
| get_cell.cl.co.ratio | Get cell co-clustering ratios |
| get_cl_df | Generate an initial cl.df object based on cl |
| get_cl_mat | Generate a sparse matrix one-hot representation of clusters x... |
| get_cl_means | Compute cluster means for each row in a matrix |
| get_cl_means_list | Title |
| get_cl_medians | Compute cluster medians for each row in a matrix |
| get_cl_present_list | Title |
| get_cl_prop | Compute cluster proportions for each row in a matrix |
| get_cl_sim | Title |
| get_cl_sim_multiple | Title |
| get_cl_sums | Compute cluster sums for each row in a matrix |
| get_core_intermediate | Get core intermediate |
| get_de_genes_sym | Get de genes sym |
| get_de_lfc_list | Title |
| get_de_matrix | Generate a matrix of pairwise DE results |
| get_dend_markers | get dendrogram precomputed markers |
| get_dend_markers_direction | get dendrogram precomputed markers (direction) |
| get_dend_parent | Get dendrogram parent |
| get_de_pair | Get de pair |
| get_de_result | Title |
| get_de_score | Get de score |
| get_eigen | Compute module eigen genes |
| get_gene_cl_correlation | Get gene cl correlation |
| get_gene_score | Title |
| get_knn | Get KNN |
| get_knn_batch | get knn batch |
| get_knn_graph | get knn graph |
| get_knn_weight | Title |
| get.markers.num | Title |
| get_pair_matrix | Subset a matrix as a vector using row and column positions |
| get_pair_matrix_coor | Convert matrix row/column positions to vector position |
| get_pairs | Convert underscore_separated pair names to a data.frame |
| get_RD_cl_center | Title |
| getTopMarkersByPropNew | Find specific marker gene for each cluster |
| group_cl | Assign clusters to a group |
| group_specific_markers | Title |
| harmonize | Harmonize |
| heatmap.3 | A modified version of heatmap.2 from the gplots package for... |
| heatmap.4 | Title |
| i_harmonize | i harmonize |
| impute_knn | Title |
| impute_knn_global | Title |
| impute_val_cor | Impute val cor |
| incrementHex | Adjust color vector |
| iter_clust | Iterative clustering algorithm for single cell RNAseq dataset |
| iter_consensus_clust | Iterative consensus clustering |
| iter_impute_knn | Title |
| jaccard | Compute jaccard distances between columns of a matrix |
| jaccard_leiden | Perform Jaccard/Leiden clustering |
| jaccard_leiden.RANN | Perform Jaccard/Louvain clustering based on RANN |
| jaccard_louvain | Perform Jaccard/Louvain clustering using Rphenograph |
| jaccard_louvain.RANN | Perform Jaccard/Louvain clustering based on RANN |
| knn_cor | KNN cor |
| knn_cosine | KNN cosine |
| knn_jaccard_louvain | KNN Jaccard Louvain |
| knn_joint | knn joint |
| label_dend | Label dendrogram |
| lm_matrix | Title |
| lm_normalize | add batch substracted median |
| logCPM | Convert a matrix of raw counts to a matrix of log2(Counts per... |
| makeColorsUnique | Make a vector of unique colors |
| makeLayerLabel | Numeric layer for annotation object |
| makeRegionLabel | Split region from roi for annotation object |
| map_by_cor | Map samples to a training dataset by correlation |
| map_cl_summary | Map a dataset to a reference, and compare existing cluster... |
| map_cv | Run a single round of cross-validation of cluster mapping... |
| map_dend | Title |
| map_dend_markers | Map dend markers |
| map_dend_membership | Title |
| mapping | Title |
| map_sampling | Perform bootstrapped mapping using a fraction of provided... |
| markers_max_tau | Title |
| markers_tau_one_vs_other | Title |
| match_cl | Compute correlations of clusters to a reference set, and get... |
| merge_cl | Merge clusters based on pairwise differential expressed... |
| merge_cl_multiple | Title |
| merge_knn_result | merge knn result |
| multiplot | Title |
| mybgplot3d | Title |
| node_specific_markers | Node specific markers |
| node_vs_sibling_markers | Node vs sibling markers |
| onestep_clust | One round of clustering in the iteractive clustering pipeline |
| pair_cor | Compute correlations between each matching row or column of... |
| perp | Title |
| perpEnd | Title |
| perpMid | Title |
| perpStart | Title |
| plot_2d_select | Title |
| plot_3d_label | Title |
| plot_3d_label_multiple | Title |
| plot_3d_select | Title |
| plot_3d_val | Title |
| plot_cl_cells | Title |
| plot_cl_heatmap | Title |
| plot_cl_heatmap4 | Title |
| plot_cl_low | Plot cl low |
| plot_cl_meta_barplot | Title |
| plot_confusion | Title |
| plot_de_lfc_num | Title |
| plot_dend | Plot dendrogram |
| plot_de_num | Title |
| plot_doublet | Plot doublet |
| plot_low_qc | Plot low-quality clusters |
| plot_markers | Title |
| plot_markers_cl_means | Plot markers cl means |
| plot_pair_matrix | Title |
| plot_RD_cl | Title |
| plot_RD_gene | Title |
| plot_RD_meta | Title |
| plot_tsne | Plot tsne |
| plot_tsne_cl | Title |
| plot_tSNE_gene | Title |
| plot_tSNE_meta | Title |
| plot_vg | Generate gene variance plots |
| prcomp.irlba | prcomp irlba |
| predict_annotate_cor | Predict annotations by cluster correlation |
| predict_knn | Title |
| predict_knn_new | Title |
| prune_dend | Prune dendrogram |
| pvclust_show_signif_gradient | Pv clust show significant gradient |
| rd_PCA | Title |
| refine_cl | Refine clusters |
| renameAndOrderClusters | Rename clusters using genes and metadata |
| reorder_cl | Reorder cluster based on hiearchical clustering of clusters... |
| reorder_dend | Reorder dendrogram |
| reorder_factor | Reorder factors of one annotation to match another |
| rescale_samples | Rescale a gene x sample matrix |
| resolve_cl | Title |
| run_consensus_clust | Wrapper function to repeatively run clustering on subsampled... |
| RunUMAP | Adapt from Seurat package |
| sample_cells | Downsample cells from each cluster |
| sample_sets_list | Sample sets lists |
| select_dend_markers | Select dend markers |
| select_joint_genes | Select joint genes |
| select_joint_markers | Title |
| select_markers | Title |
| select_markers_pair | Title |
| select_markers_pair_direction | Title |
| select_markers_pair_group | Title |
| select_N_markers | Title |
| select_node_specific_markers | Select node specific markers |
| select_pos_dend_markers | Select pos dend markers |
| select_pos_markers | Title |
| set_pair_matrix | Update a matrix with values from a 1d vector using row and... |
| sim_knn | Sim knn |
| simple_dend | Simple dendrogram |
| sparse_cor | Compute correlation scores for columns of a sparse matrix |
| summarize_cl | Title |
| test_knn | Test knn |
| test_merge | Title |
| unbranch_by_conf | Unbranch by conf |
| unbranch_by_length | Unbranch by length |
| updateSampDat | Update cluster names in annotation data frame |
| vec_chisq_test | Vectorized Chi-squared tests for differential gene detection |
| within_group_specific_markers | Title |
